Variant 19-48491478-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001388485.1(LMTK3):c.4154C>T(p.Thr1385Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000789 in 1,268,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 7.9e-7 ( 0 hom. )

Consequence

LMTK3
NM_001388485.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.85

Variant links:

Genes affected

LMTK3 (HGNC:19295): (lemur tyrosine kinase 3) Predicted to enable protein kinase activity. Predicted to be involved in protein phosphorylation. Predicted to be located in Golgi membrane; axon; and dendrite. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LMTK3 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.33434576).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMTK3	NM_001388485.1 linkuse as main transcript	c.4154C>T	p.Thr1385Met	missense_variant	13/15	ENST00000600059.6	NP_001375414.1
LMTK3	NM_001080434.2 linkuse as main transcript	c.4154C>T	p.Thr1385Met	missense_variant	14/16		NP_001073903.2
LMTK3	XM_011526411.3 linkuse as main transcript	c.4232C>T	p.Thr1411Met	missense_variant	14/16		XP_011524713.1	A0A3B3ISL5
LMTK3	XM_011526412.3 linkuse as main transcript	c.4199C>T	p.Thr1400Met	missense_variant	14/16		XP_011524714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMTK3	ENST00000600059.6 linkuse as main transcript	c.4154C>T	p.Thr1385Met	missense_variant	13/15	2	NM_001388485.1	ENSP00000472020.1		Q96Q04

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

7.89e-7

AC:

AN:

1268106

Hom.:

Cov.:

AF XY:

0.00000161

AC XY:

AN XY:

619212

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000171

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 15, 2024

The c.4241C>T (p.T1414M) alteration is located in exon 14 (coding exon 14) of the LMTK3 gene. This alteration results from a C to T substitution at nucleotide position 4241, causing the threonine (T) at amino acid position 1414 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.079

BayesDel_noAF

Benign

-0.35

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0092

T;.;.

Eigen

Uncertain

0.20

Eigen_PC

Benign

0.20

FATHMM_MKL

Uncertain

0.77

LIST_S2

Benign

0.60

T;T;T

M_CAP

Pathogenic

0.61

MetaRNN

Benign

0.33

T;T;T

MetaSVM

Benign

-0.64

MutationAssessor

Benign

1.4

L;.;.

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

-1.5

.;N;.

REVEL

Benign

0.24

Sift

Benign

0.036

.;D;.

Sift4G

Uncertain

0.032

D;D;.

Polyphen

1.0

D;.;.

Vest4

0.41

MutPred

0.26

Loss of glycosylation at T1385 (P = 4e-04);.;.;

MVP

0.62

ClinPred

0.87

GERP RS

3.5

Varity_R

0.071

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over